Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/39/f11e193fef367811bf3a02d54f5985/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_6GF-N1-BDNA-1_A23NMNVLT4_1/1136_6GF-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/foresight/xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/39/f11e193fef367811bf3a02d54f5985/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_6GF-N1-BDNA-1_A23NMNVLT4_1/1136_6GF-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_6GF-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1136_6GF-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
The index file is older than the data file: 1136_6GF-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_6GF-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Reads: 40594966 total, 28263 skipped (flags/unmapped)
Fragments: 20337702 total (20213648 tlen-paired, 1890 hash-paired, 143 singletons, 4973 discordant, 117048 orphans, 4245 too large [>5000 bp], 5270480 duplicates)
Reads: 44077484 total, 23129 skipped (flags/unmapped)
Fragments: 22084333 total (21957944 tlen-paired, 1076 hash-paired, 228 singletons, 3548 discordant, 121537 orphans, 3727 too large [>5000 bp], 5612043 duplicates)
Reads: 48175978 total, 25717 skipped (flags/unmapped)
Fragments: 24139365 total (23985841 tlen-paired, 1449 hash-paired, 168 singletons, 5150 discordant, 146757 orphans, 9228 too large [>5000 bp], 6290653 duplicates)
Reads: 48497592 total, 44599 skipped (flags/unmapped)
Fragments: 24345712 total (23975708 tlen-paired, 1986 hash-paired, 196 singletons, 71703 discordant, 296119 orphans, 28942 too large [>5000 bp], 6356706 duplicates)